Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG

Basic information

species Zea mays
transcript GRMZM2G114861_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g53760.2 (Oryza sativa), 3'ss of exon 13
tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctctattgggtctga--taatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
   |   |  |     | | |  ||  ||   |  |     |    | |   | |||||||||   | || |||| |  |  | ||  |  ||||  |  ||||||||||||| ||| || ||||||||||| || ||| | || |||||||| |||||| | |||||||||||||| || |||
--tacaagctagcacttattatctgaattcacatgtgtctgttagccacctagtctacatatcaacagtgagtctaaattttttttcaccacattgaaccagGTCTGTGGGTAGGACCCAAATGAATGAACAATCTTCCCGGAGCCATTTTGTTTTCACACTGAAGATATCTGGATCAAATGAG

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G34330.1 (Glycine max), 3'ss of exon 12
tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctctattgggtctgataatgttatctgcatttcaat-agGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
||| |   | |   ||| |  | |   || ||  |  |   || |   || || ||    |  |  | |    ||     || | | |   || |  | || |||||||| || ||||||||||||||||| || || ||||||||||||||||||||  |     ||| |||    || |||
tag-tgcaataaaatattttgatttatttacttctagaaggtaaaatcctttgcctttggaggttaaatttaactatatttgcttttttttttccttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGATTATATGGTGTAAATGAG

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G16580.1 (Glycine max), 3'ss of exon 13
tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactaca---tatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
   ||   |||   |||  |       | ||||| |   || | | || | |   | ||   || || |||||  |    |  |  | | | | |     ||| ||||||||||| || |||||||||||||| || || ||||||||||||||||||||  |    ||||  ||    || |||
---atggaacaaaatattgatttattttctctaagtagtcacaaaactttttatttccaacttaactgtattgatttctttctttctgtttacctccttttagATCTGTGGGTAAAACCCAGATGAATGAACAATCATCAAGAAGTCATTTTGTATTCACTCTTCGAATATACGGTGTAAATGAG

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 12
-tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
  | || |    |||| |       |       || ||   |  | | | |||  | ||  | || |||||  |    |  |  |   |   |     ||| |||||||| || || |||||||||||||| || || ||||||||||||||||||||  |    ||||  ||    || |||
caaaatattgatttgttttctcttagtagccacaactctcaacctttttatgtc-caactcaactttattgatttatttttttcttgttatctccttttagATCTGTGGGAAAAACCCAGATGAATGAACAATCATCAAGAAGTCATTTTGTATTCACTCTTCGAATATACGGTGTAAATGAG

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 13
tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctcta--ttgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
    |   | |   ||| |  | |   || ||  |  |   ||||   || || ||    || |  |  ||   | |  |    || | |   |||   ||| |||||||| || ||||||||||||||||| || || ||||||||||||||||||||  |    |||| |||    || |||
--agtgcaataaaatattttgatttatttacttctagaaattataatcctttgcctttggatgttgaatttaactatatttgctttctttttgtttttttagATCTGTGGGAAAAACTCAGATGAATGAACAATCTTCTAGAAGTCATTTTGTATTCACTCTTCGAATATATGGTGTAAATGAG

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 13
----tagatctgacattgtatctaaaatggcttt-ctaattcagcatatatctctgtgactacatatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
    || | |||| |     |  ||  || ||   |||| |   |||  |  | |  ||  |   |||| | |      ||| | |  | |      |||   |||||||| || |||||||||||||| || || || |||||||| |||||||| |||||  |||  || |||||   |||||||
gcaatatagctgaaacccgtttcaatttgactgaactaaatggccatcaagattttcgatga---atctttctgacagttgaaagttgttttctttcttcttcagGTCTGTAGGGAAGACTCAGATGAACGAGCAATCTTCCAGAAGCCATTTTGTTTTCACGCTAAGAATCTCTGGTGTTAACGAG

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 12
tagatctga---cattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
|| |  ||    |||||| | |    |    ||| | | |||  | |||   |  |   |||    |  |   | |   | | ||| | | |  |     |||||||||||| || || ||||||||||| || || ||||||||||||||||| |||||  |   |||||||||   ||| |||
tacacttgggtgcattgtcttttgtttaaaattcca-tgcagtttgtatacttcagttcacaaggattca--agattataaattgtcacccgtttccttttagGTCTGTGGGCAAAACACAGATGAATGAGCAATCATCCAGAAGTCATTTTGTGTTCACTCTGCGGATATCTGGTGTTAATGAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67019346|gb|CO448095.1|CO448095
EST:     TTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAG                         GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGT
genomic: TTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGT
EST: gi|67014413|gb|CO443162.1|CO443162
EST:     TTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAG                         GTCTGTGTGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGT
genomic: TTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGT
EST: gi|78085386|gb|DV513779.1|DV513779
EST:     TTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAG                         GTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGT
genomic: TTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

AGCATGACCCTCATGGGAATATTGTGTCGGACCTTACAATTATTGATGTCTTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 29

AGCATGACCCTCATGGGAATATTGTGTCGGACCTTACAATTATTGATGTCTTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 42

AGCATGACCCTCATGGGAATATTGTGTCGGACCTTACAATTATTGATGTCTTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

AGCATGACCCTCATGGGAATATTGTGTCGGACCTTACAATTATTGATGTCTTTGGTATTGCTGATGTGACTAGTCTACTAGAGAAAGCATCCCAGAGTAGgtgagtcatt ... atttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgtgactacatatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG
                          gtctgat  putative branch site (score: 218)
                               ataatgttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatctgacattgtatctaaaatggctttctaattcagcatatatctctgtgactacatatctctattgggtctgataatgttatctgcatttcaatagGTCTGTGGGTAAGACTCAGATGAATGAACAGTCGTCCAGAAGTCATTTTGTATTCACATTAAAGATATCTGGATCTAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - tgacatt
- - - - - - - - - - - - - - - - - ttcagca